Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
input MCF7 vehicle
cell line
MCF7
source tissue
mammary gland, breast; derived from metastatic site: pleural effusion
treatment
Vehicle (ethanol) 1h
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MCF7 cells were crosslinked, chromatin from nuclear lisates was sonicated and protein-DNA complexes were isolated with antibody. Input samples correspond to 10% of the material before antibody isolation. Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to the manufacturer's instructions. NEBNext Multiplex Oligos for Illumina were used during library amplification

Sequencing Platform

instrument_model
NextSeq 550

hg38

Number of total reads
43221132
Reads aligned (%)
99.0
Duplicates removed (%)
3.9
Number of peaks
1188 (qval < 1E-05)

hg19

Number of total reads
43221132
Reads aligned (%)
98.0
Duplicates removed (%)
5.4
Number of peaks
1054 (qval < 1E-05)

Base call quality data from DBCLS SRA